<h1 class="title" id="page-title">Gene Assignment database</h1>

The gene assignment database includes two binary files: 

<ul>
    <li><a href="http://pongor.itk.ppke.hu/~roberto/geneassignment/taxoner_DB.bin">taxoner_DB.bin</a>: the binary file with the GenBank info</li>
    <li><a href="http://pongor.itk.ppke.hu/~roberto/geneassignment/taxoner_DB.ind">taxoner_DB.ind</a>: an index with the GenBank Gi and the offset in the taxoner_DB.bin</li>
</ul>

<p>
    This two files should be copied to the folder: <i>databases/geneassignment/</i> on the Taxoner folder or run:
</p>

<pre>
cd databases/
wget -r --reject "index.html*" -e robots=off -np -nH --cut-dirs=1 http://pongor.itk.ppke.hu/~roberto/geneassignment/
</pre>

<p>
    The files were created using this text file 
    <a href="http://pongor.itk.ppke.hu/~roberto/geneassignment/taxoner_DB.txt.gz">
        taxoner_DB.txt.gz
    </a>. This text file is created using a 
    <a href="http://taxoner.googlecode.com/svn/trunk/Taxoner/src/cgassignment/create_Taxoner_DB.sql">
        SQL script
    </a> on the 
    <a href="http://code.google.com/p/jbiowh/">
        JBioWH        
    </a> relational schema with the modules GenBank, ProtClust and EGGNog inserted.
</p>

<p>
    To create the binary files:
</p>
<ol>
    <li>Create the <i>taxoner_DB.txt</i> file:<br>
        <ul>
            <li>Install the JBioWH relational schema. See <a href="http://code.google.com/p/jbiowh/wiki/InstallationGuide">the installation guide</a></li>
            <li>Load the Taxonomy database. See <a href="http://code.google.com/p/jbiowh/wiki/TaxonomyCF">the guide</a></li>
            <li>Load the GenBank database. See <a href="http://code.google.com/p/jbiowh/wiki/GenBankCF">the guide</a></li>
            <li>Load the NCBI Protein Cluster database. See <a href="http://code.google.com/p/jbiowh/wiki/NCBIProtClustCF">the guide</a></li>
            <li>Load the COG and EGGNog databases. See <a href="http://code.google.com/p/jbiowh/wiki/COGCF">the guide</a></li>
            <li>Execute the <i>create_Taxoner_DB.sql</i> script on your server
                <pre>
    mysql biowh < create_Taxoner_DB.sql   
                </pre>
                Copy the file <i>/tmp/taxoner_DB.txt</i> to your home.
            </li>
        </ul>
    </li>
    <li>
        Run the <i>cgassignment</i> program to create the binary files from the Taxoner folder
        <pre> 
    ./bin/cgassignment -w -t ~/taxoner_DB.txt -b databases/taxoner_DB.bin -i databases/taxoner_DB.ind
        </pre>
    </li>
</ol>

